GM12878细胞、GM12878 人B淋巴细胞

GM12878、GM12878、GM12878GM12878 人B淋巴细胞

Cell line name GM12878

Synonyms GM-12878

Accession CVCL_7526

Resource Identification Initiative To cite this cell line use: GM12878 (RRID:CVCL_7526)

Comments Part of: CEPH/Utah pedigree cell line collection.

Part of: ENCODE project common cell types; tier 1.

Part of: Genetic Testing Reference Material (GeT-RM) samples.

Part of: Genome in a Bottle (GIAB) consortium samples.

Part of: International Genome Sample Resource (1000 genomes project) cell lines.

Registration: CEPH Families Reference Panel; 146302.

Registration: National Institute of Standards and Technology, Standard Reference Materials; HG001.

Population: Caucasian; Utah residents with ancestry from Northern and Western Europe.

Transformant: NCBI_TaxID; 10376; Epstein-Barr virus (EBV).

Omics: CAGE-seq analysis.

Omics: CTCF ChIP-seq epigenome analysis.

Omics: H3K27ac ChIP-seq epigenome analysis.

Omics: H3K27me3 ChIP-seq epigenome analysis.

Omics: H3K36me3 ChIP-seq epigenome analysis.

Omics: H3K4me1 ChIP-seq epigenome analysis.

Omics: H3K4me2 ChIP-seq epigenome analysis.

Omics: H3K4me3 ChIP-seq epigenome analysis.

Omics: H3K79me2 ChIP-seq epigenome analysis.

Omics: H3K9ac ChIP-seq epigenome analysis.

Omics: H3K9me3 ChIP-seq epigenome analysis.

Omics: H4K20me1 ChIP-seq epigenome analysis.

Omics: YY1 ChIP-seq epigenome analysis.

Omics: CNV analysis.

Omics: Deep exome analysis.

Omics: Deep proteome analysis.

Omics: DNA methylation analysis.

Omics: Genome sequenced.

Omics: Mitochondrial genome sequenced.

Omics: SNP array analysis.

Omics: Transcriptome analysis by microarray.

Omics: Transcriptome analysis by RNAseq.

Derived from site: In situ; Peripheral blood; UBERON=UBERON_0000178.

Sequence variations

Mutation; HGNC; 2621; CYP2C19; Simple; p.Pro227Pro (c.681G>A); ClinVar=VCV000016897; Zygosity=Unspecified; Note=Cryptic splice acceptor activation. CYP2C19*2 allele (Coriell=GM12878).

HLA typing Source: PubMed=27792722

Class I

HLA-A A*01,11

HLA-B B*08,56

HLA-C C*01,07

Class II

HLA-DP DPA1*01:03:01,02:01:01

DPB1*04:01:01,14:01

HLA-DQ DQA1*01,05

DQB1*02,05

HLA-DR DRB1*01,03:01

Species of origin Homo sapiens (Human) (NCBI Taxonomy: 9606)

Hierarchy Children:

CVCL_N800 (GM12878-XiMat clone 16) CVCL_N801 (GM12878-XiMat clone 56)

Sex of cell Female

Age at sampling Age unspecified

Category Transformed cell line

Publications

PubMed=17122850; DOI=10.1038/nature05329; PMCID=PMC2669898

Redon R., Ishikawa S., Fitch K.R., Feuk L., Perry G.H., Andrews T.D., Fiegler H., Shapero M.H., Carson A.R., Chen W.-W., Cho E.K., Dallaire S., Freeman J.L., Gonzalez J.R., Gratacos M., Huang J., Kalaitzopoulos D., Komura D., MacDonald J.R., Marshall C.R., Mei R., Montgomery L., Nishimura K., Okamura K., Shen F., Somerville M.J., Tchinda J., Valsesia A., Woodwark C., Yang F.-T., Zhang J.-J., Zerjal T., Zhang J., Armengol L., Conrad D.F., Estivill X., Tyler-Smith C., Carter N.P., Aburatani H., Lee C., Jones K.W., Scherer S.W., Hurles M.E.

Global variation in copy number in the human genome.

Nature 444:444-454(2006)

 

PubMed=19043577; DOI=10.1371/journal.pgen.1000287; PMCID=PMC2583954

Choy E., Yelensky R., Bonakdar S., Plenge R.M., Saxena R., De Jager P.L., Shaw S.Y., Wolfish C.S., Slavik J.M., Cotsapas C., Rivas M.A., Dermitzakis E.T., Cahir-McFarland E., Kieff E.D., Hafler D.A., Daly M.J., Altshuler D.M.

Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines.

PLoS Genet. 4:E1000287-E1000287(2008)

 

PubMed=20856902; DOI=10.1371/journal.pbio.1000480; PMCID=PMC2939022

Cheung V.G., Nayak R.R., Wang I.X.-R., Elwyn S., Cousins S.M., Morley M., Spielman R.S.

Polymorphic cis- and trans-regulation of human gene expression.

PLoS Biol. 8:e1000480.1-e1000480.14(2010)

 

PubMed=21418647; DOI=10.1186/gb-2011-12-3-r25; PMCID=PMC3129675

Morcos L., Ge B., Koka V., Lam K.C.L., Pokholok D.K., Gunderson K.L., Montpetit A., Verlaan D.J., Pastinen T.

Genome-wide assessment of imprinted expression in human cells.

Genome Biol. 12:R25.1-R25.14(2011)

 

PubMed=23325432; DOI=10.1101/gr.147942.112; PMCID=PMC3589544

Varley K.E., Gertz J., Bowling K.M., Parker S.L., Reddy T.E., Pauli-Behn F., Cross M.K., Williams B.A., Stamatoyannopoulos J.A., Crawford G.E., Absher D.M., Wold B.J., Myers R.M.

Dynamic DNA methylation across diverse human cell lines and tissues.

Genome Res. 23:555-567(2013)

 

PubMed=23676674; DOI=10.1038/nature12223; PMCID=PMC3789121

Wu L.-F., Candille S.I., Choi Y., Xie D., Jiang L.-H., Li-Pook-Than J., Tang H., Snyder M.P.

Variation and genetic control of protein abundance in humans.

Nature 499:79-82(2013)

 

PubMed=24185094; DOI=10.1038/nbt.2728; PMCID=PMC4180835

Selvaraj S., Dixon J.R., Bansal V., Ren B.

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.

Nat. Biotechnol. 31:1111-1118(2013)

 

PubMed=24380390; DOI=10.1186/gb-2013-14-12-r148; PMCID=PMC4056453

Schwalie P.C., Ward M.C., Cain C.E., Faure A.J., Gilad Y., Odom D.T., Flicek P.

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.

Genome Biol. 14:R148.1-R148.15(2013)

 

PubMed=26719794; DOI=10.1186/s13742-015-0106-1; PMCID=PMC4696294

Teo A.S.M., Verzotto D., Yao F., Nagarajan N., Hillmer A.M.

Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.

GigaScience 4:65.1-65.6(2015)

 

PubMed=26621101; DOI=10.1016/j.jmoldx.2015.08.005; PMCID=PMC4695224

Pratt V.M., Everts R.E., Aggarwal P., Beyer B.N., Broeckel U., Epstein-Baak R., Hujsak P., Kornreich R., Liao J., Lorier R., Scott S.A., Smith C.-Y.H., Toji L.H., Turner A., Kalman L.V.

Characterization of 137 genomic DNA reference materials for 28 pharmacogenetic genes: a GeT-RM collaborative project.

J. Mol. Diagn. 18:109-123(2016)

 

PubMed=27792722; DOI=10.1371/journal.pcbi.1005151; PMCID=PMC5085092

Dilthey A.T., Gourraud P.-A., Mentzer A.J., Cereb N., Iqbal Z., McVean G.A.T.

High-accuracy HLA type inference from whole-genome sequencing data using population reference graphs.

PLoS Comput. Biol. 12:e1005151.1-e1005151.16(2016)

 

CLPUB00604

Chow S.

Targeted capture and sequencing of immunoglobulin rearrangements in multiple myeloma to enable detection of minimal residual disease.

Thesis MSc (2017); University of Toronto; Toronto; Canada

 

PubMed=29116076; DOI=10.1038/s41467-017-01467-7; PMCID=PMC5677018

Garieri M., Delaneau O., Santoni F.A., Fish R.J., Mull D., Carninci P., Dermitzakis E.T., Antonarakis S.E., Fort A.

The effect of genetic variation on promoter usage and enhancer activity.

Nat. Commun. 8:1358.1-1358.9(2017)